Reproducibility by Daniel P. Morreale
Figure showing the concepts!
Genome Annotation
In bioinformatics, genome annotation is a multi-level process that identifies and labels all the relevant features on a genome sequence in order to generate a blueprint for the potential roles and capabilities of an organism.
This process includes Prediction of :
- protein-coding genes and their putative products (minimum)
- other functional genome units
- structural RNAs
- tRNAs,
- small RNAs
- pseudogenes
- control regions
- direct and inverted repeats
- insertion sequences
- transposons
- other mobile elements.
There are various online annotation servers (also available as command-line). Couple of examples:
- The NCBI Prokaryotic Genome Annotation Pipeline (PGAP).
- Rapid Annotation using Subsystem Technology (RAST).
In this course, we will use Prokka. However, I would highly encourage using Bakta for future work. We chose Prokka as Bakta DB is large to download for the course.
Let's annotate the genome that we assembled last time. What is the number of CDS (Hint: check .faa file)?
conda activate prokka
cd ~/MGJW/problem_set3/out_S56
prokka contigs.fa
Let's annotate a better assembled genome with more options.
prokka -h
cd ~/MGJW/problem_set1/fasta
prokka --outdir annot_genome4 --kingdom Bacteria --locustag genom4 --prefix genome4 genome4.fasta
ABRicate is a tool for mass screening of contigs for antimicrobial resistance, virulence genes or genes of interest. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. You can also make your own database.
conda activate abricate
cd annot_genome4
abricate -db vfdb genome4.fna
abricate genome4.fna
- Standard for reporting bacterial genome sequences Minimum completeness and maximum contamination.
- Review: Contamination detection in genomic data